3CKC - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   B. THETAIOTAOMICRON SUSD

Authors :   N. M. Koropatkin, E. C. Martens, J. I. Gordon, T. J. Smith

Date :   14 Mar 08 (Deposition) - 01 Apr 08 (Release) - 06 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Tpr Repeat, Carbohydrate Binding, Starch Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. M. Koropatkin, E. C. Martens, J. I. Gordon, T. J. Smith
Starch Catabolism By A Prominent Human Gut Symbiont Is Directed By The Recognition Of Amylose Helices.
Structure V. 16 1105 2008
PubMed-ID: 18611383 | Reference-DOI: 10.1016/J.STR.2008.03.017

Molecule 1 - SUSD
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 26-551
	Gene	:	SUSD
	Organism Scientific	:	BACTEROIDES THETAIOTAOMICRON
	Organism Taxid	:	226186
	Strain	:	VPI-5482

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 19)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	EDO	12	Ligand/Ion	1,2-ETHANEDIOL
4	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (4, 7)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
4	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
4	MES	-1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:273 , GLN A:288 , ASP A:430 , ASP A:432	BINDING SITE FOR RESIDUE CA A 600
02	AC2	SOFTWARE	ASP B:273 , GLN B:288 , ASP B:430 , ASP B:432	BINDING SITE FOR RESIDUE CA B 700
03	AC3	SOFTWARE	TYR A:52 , GLY A:216 , ARG A:217	BINDING SITE FOR RESIDUE EDO A 901
04	AC4	SOFTWARE	TYR A:52 , ALA A:53 , GLY A:56 , ILE A:286 , ARG A:287	BINDING SITE FOR RESIDUE EDO A 902
05	AC5	SOFTWARE	TYR A:416 , GLU B:358	BINDING SITE FOR RESIDUE EDO A 903
06	AC6	SOFTWARE	TYR B:52 , GLY B:216	BINDING SITE FOR RESIDUE EDO B 904
07	AC7	SOFTWARE	GLN B:72 , ARG B:81 , ASN B:85 , ARG B:118 , TYR B:301	BINDING SITE FOR RESIDUE EDO B 905
08	AC8	SOFTWARE	GLY B:127 , ILE B:130 , THR B:131 , PRO B:174	BINDING SITE FOR RESIDUE EDO B 906
09	AC9	SOFTWARE	ASP A:273 , GLN A:288 , ASP A:289 , ASP A:430	BINDING SITE FOR RESIDUE EDO A 907
10	BC1	SOFTWARE	ASP B:273 , GLN B:288 , ASP B:289 , ASP B:430	BINDING SITE FOR RESIDUE EDO B 908
11	BC2	SOFTWARE	ASP A:145 , ASP B:273 , MET B:279	BINDING SITE FOR RESIDUE EDO B 909
12	BC3	SOFTWARE	TYR B:510 , LEU B:511	BINDING SITE FOR RESIDUE EDO B 910
13	BC4	SOFTWARE	ALA A:518 , MET A:519 , GLY B:517	BINDING SITE FOR RESIDUE EDO B 911
14	BC5	SOFTWARE	ALA B:328 , GLN B:331 , GLN B:397 , ASP B:513	BINDING SITE FOR RESIDUE EDO B 912
15	BC6	SOFTWARE	ASP A:73 , ASN A:295 , ASN A:318 , TRP A:320	BINDING SITE FOR RESIDUE MES A 1000
16	BC7	SOFTWARE	ASP A:273 , ARG A:287 , GLN A:288 , ASP A:289 , LYS A:292 , ASP A:432	BINDING SITE FOR RESIDUE PEG A 800
17	BC8	SOFTWARE	ASP B:273 , ARG B:287 , GLN B:288 , ASP B:289 , LYS B:292 , ASP B:432	BINDING SITE FOR RESIDUE PEG B 801

(no "SS Bond" information available for 3CKC)

(no "Cis Peptide Bond" information available for 3CKC)

(no "SAP(SNP)/Variant" information available for 3CKC)

(no "PROSITE Motif" information available for 3CKC)

(no "Exon" information available for 3CKC)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:501
 aligned with SUSD_BACTN | Q8A1G2 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:511
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550 
           SUSD_BACTN    41 SFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
               SCOP domains d3ckca_ A: Starch u          tilization system protein SusD                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------3ckcA02 A:210-307,A:412-490  [code=1.25.40.10, no name defined]                                   3ckcA03 A:308-411 SusD-like                                                                             3ckcA02 A:210-307,A:412-490  [code=1.25.40.10, no name defined]                ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....----------........hhhhhhhhhhhh....eee......hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhheeee.........eeeehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhh.....hhhhhh.eeeee..hhhhhh..hhhhhhhhh.................eeehhhhhh....hhhhh...............hhhhhhhhhhhh..hhhhhhhhhh.....ee................hhhhh.ee......................eeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhh...........hhhhh......hhhhhh...hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ckc A  41 SFDQQGVFVKGYAMLGVTG----------DGQDEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWScIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
                                    50        |-        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320 |     330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550 
                                             59         70                                                                                                                                                                                                                                                         322-CSO

Chain B from PDB  Type:PROTEIN  Length:500
 aligned with SUSD_BACTN | Q8A1G2 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:510
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551
           SUSD_BACTN    42 FDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
               SCOP domains d3ckcb_ B: Starch           utilization system protein SusD                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------3ckcB02 B:210-307,B:412-490  [code=1.25.40.10, no name defined]                                   3ckcB03 B:308-411 SusD-like                                                                             3ckcB02 B:210-307,B:412-490  [code=1.25.40.10, no name defined]                ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....----------........hhhhhhhhhhhh....eee......hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhheeee.........eeeehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhh.....hhhhhh.eeeee..hhhhhh..hhhhhhhhh.................eeehhhhhh....hhhhh...............hhhhhhhhhhhh..hhhhhhhhhh.....ee................hhhhh.ee......................eeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhh...........hhhhh......hhhhhh...hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ckc B  42 FDQQGVFVKGYAMLGVTG----------DGQDEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWScIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
                                    51       | -        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321|      331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551
                                            59         70                                                                                                                                                                                                                                                         322-CSO

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: alpha-alpha superhelix (690)

Superfamily: TPR-like (83)

Family: SusD-like (7)

Protein domain: Starch utilization system protein SusD (5)

Bacteroides thetaiotaomicron [TaxId: 818] (5)

1a	d3ckca_	A:
1b	d3ckcb_	B:

(no "Pfam Domain" information available for 3CKC)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SUSD_BACTN | Q8A1G2)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:2001070	starch binding	Interacting selectively and non-covalently with starch.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0005983	starch catabolic process	The chemical reactions and pathways resulting in the breakdown of starch, the most important reserve polysaccharide in plants.
	GO:0005982	starch metabolic process	The chemical reactions and pathways involving starch, the most important reserve polysaccharide in plants. It is a glucan consisting of two components, amylose and amylopectin, which are both glucose homopolymers. Starch is synthesized as a temporary storage form of carbon and can be catabolized to produce sucrose.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019867	outer membrane	The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ckc)

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	3ckc
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	SUSD_BACTN \| Q8A1G2
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UniProtKB/Swiss-Prot
	SUSD_BACTN \| Q8A1G2	:	3ck7 3ck8 3ck9 3ckb

3ck7	B. THETAIOTAOMICRON SUSD WITH ALPHA-CYCLODEXTRIN
3ck8	B. THETAIOTAOMICRON SUSD WITH BETA-CYCLODEXTRIN
3ck9	B. THETAIOTAOMICRON SUSD WITH MALTOHEPTAOSE
3ckb	B. THETAIOTAOMICRON SUSD WITH MALTOTRIOSE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 19)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (2, 4)

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Gene Ontology (9, 9)

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